Explore Workflows
View already parsed workflows here or click here to add your own
Graph | Name | Retrieved From | View |
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picard_markduplicates
Mark duplicates |
https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/subworkflows/picard_markduplicates.cwl Branch/Commit ID: c494fa4f60d9215842c4d2c75ed7d89757435b0f |
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bwa_index
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https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/subworkflows/bwa_index.cwl Branch/Commit ID: c494fa4f60d9215842c4d2c75ed7d89757435b0f |
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SSU-from-tablehits.cwl
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https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git
Path: tools/SSU-from-tablehits.cwl Branch/Commit ID: 9c57dba558a4e04a1884eae1df8431dcaccafc1e |
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tt_univec_wnode.cwl
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https://github.com/ncbi/pgap.git
Path: task_types/tt_univec_wnode.cwl Branch/Commit ID: 1e7aa9f0c34987ddafa35f9b1d2c77d99fafbdab |
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FASTQ Vector Removal
This workflow clean up vectros from fastq files |
https://github.com/ncbi/cwl-ngs-workflows-cbb.git
Path: workflows/Contamination/fastq-vector-removal.cwl Branch/Commit ID: 11f70a71cb68b3960c2d410ba1fdcd3b8a7e1419 |
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Illumina read quality control, trimming and contamination filter.
**Workflow for Illumina paired read quality control, trimming and filtering.**<br /> Multiple read pairs will be merged into single paired dataset.<br /> Summary: - FastQC on raw data files<br /> - fastp for read quality trimming<br /> - Kraken2 for taxonomic classification of reads<br /> - BBduk for phix and rRNA filtering<br /> - BBmap for (contamination) filtering using given references<br /> - FastQC on filtered (merged) data<br /> **All tool CWL files and other workflows can be found here:**<br> Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl<br> Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows<br> WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default |
https://git.wur.nl/unlock/cwl.git
Path: cwl/workflows/workflow_illumina_quality.cwl Branch/Commit ID: 60fafdfbec9b39c860945ef4634e0c28cb5e976c |
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align_sort_sa
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https://github.com/ncbi/pgap.git
Path: task_types/tt_align_sort_sa.cwl Branch/Commit ID: 505b91e41741ccbcd5ebd2b6a09a3be604f9ece3 |
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Non-Coding Bacterial Genes
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https://github.com/ncbi/pgap.git
Path: bacterial_noncoding/wf_bacterial_noncoding.cwl Branch/Commit ID: 5cc4af517f82f4cda3023644d61abd85cbc1fc18 |
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Apply filters to VCF file
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/filter_vcf_mouse.cwl Branch/Commit ID: 6b365b79675b2aabfb8d5829bb8df0a6e986b037 |
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qiime2 rarefaction visualization
Alpha rarefaction plotting from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/ |
https://github.com/duke-gcb/bespin-cwl.git
Path: packed/qiime2-step3-alpha-analysis.cwl Branch/Commit ID: e2dc95d4f12210359360d814382e7201d836dfcf Packed ID: qiime2-07-alpha-rarefaction.cwl |